src/jalview/jbgui/GPreferences.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.jbgui;
  22
  23 import jalview.fts.core.FTSDataColumnPreferences;
  24 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
  25 import jalview.fts.service.pdb.PDBFTSRestClient;
  26 import jalview.gui.JvSwingUtils;
  27 import jalview.gui.StructureViewer.ViewerType;
  28 import jalview.util.MessageManager;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.Color;
  32 import java.awt.Component;
  33 import java.awt.Dimension;
  34 import java.awt.FlowLayout;
  35 import java.awt.Font;
  36 import java.awt.GridBagConstraints;
  37 import java.awt.GridBagLayout;
  38 import java.awt.GridLayout;
  39 import java.awt.Insets;
  40 import java.awt.Rectangle;
  41 import java.awt.event.ActionEvent;
  42 import java.awt.event.ActionListener;
  43 import java.awt.event.FocusEvent;
  44 import java.awt.event.KeyEvent;
  45 import java.awt.event.MouseAdapter;
  46 import java.awt.event.MouseEvent;
  47
  48 import javax.swing.AbstractCellEditor;
  49 import javax.swing.BorderFactory;
  50 import javax.swing.ButtonGroup;
  51 import javax.swing.DefaultListCellRenderer;
  52 import javax.swing.JButton;
  53 import javax.swing.JCheckBox;
  54 import javax.swing.JComboBox;
  55 import javax.swing.JFileChooser;
  56 import javax.swing.JLabel;
  57 import javax.swing.JPanel;
  58 import javax.swing.JRadioButton;
  59 import javax.swing.JScrollPane;
  60 import javax.swing.JTabbedPane;
  61 import javax.swing.JTable;
  62 import javax.swing.JTextField;
  63 import javax.swing.ListSelectionModel;
  64 import javax.swing.SwingConstants;
  65 import javax.swing.border.Border;
  66 import javax.swing.border.EmptyBorder;
  67 import javax.swing.border.EtchedBorder;
  68 import javax.swing.border.TitledBorder;
  69 import javax.swing.event.ChangeEvent;
  70 import javax.swing.event.ChangeListener;
  71 import javax.swing.table.TableCellEditor;
  72 import javax.swing.table.TableCellRenderer;
  73
  74 /**
  75  * Base class for the Preferences panel.
  76  *
  77  * @author $author$
  78  * @version $Revision$
  79  */
  80 public class GPreferences extends JPanel
  81 {
  82   private static final Font LABEL_FONT = JvSwingUtils.getLabelFont();
  83
  84   private static final Font LABEL_FONT_ITALIC = JvSwingUtils.getLabelFont(
  85           false, true);
  86
  87   /*
  88    * Visual tab components
  89    */
  90   protected JCheckBox fullScreen = new JCheckBox();
  91
  92   protected JCheckBox openoverv = new JCheckBox();
  93
  94   protected JCheckBox seqLimit = new JCheckBox();
  95
  96   protected JCheckBox rightAlign = new JCheckBox();
  97
  98   protected JComboBox<String> fontSizeCB = new JComboBox<String>();
  99
 100   protected JComboBox<String> fontStyleCB = new JComboBox<String>();
 101
 102   protected JComboBox<String> fontNameCB = new JComboBox<String>();
 103
 104   protected JCheckBox showOccupancy = new JCheckBox();
 105
 106   protected JCheckBox showUnconserved = new JCheckBox();
 107
 108   protected JCheckBox idItalics = new JCheckBox();
 109
 110   protected JCheckBox smoothFont = new JCheckBox();
 111
 112   protected JCheckBox scaleProteinToCdna = new JCheckBox();
 113
 114   protected JComboBox<String> gapSymbolCB = new JComboBox<String>();
 115
 116   protected JCheckBox wrap = new JCheckBox();
 117
 118   protected JComboBox<String> sortby = new JComboBox<String>();
 119
 120   protected JComboBox<String> sortAnnBy = new JComboBox<String>();
 121
 122   protected JComboBox<String> sortAutocalc = new JComboBox<String>();
 123
 124   protected JCheckBox startupCheckbox = new JCheckBox();
 125
 126   protected JTextField startupFileTextfield = new JTextField();
 127
 128   // below are in the 'second column'
 129   protected JCheckBox annotations = new JCheckBox();
 130
 131   protected JCheckBox quality = new JCheckBox();
 132
 133   protected JCheckBox conservation = new JCheckBox();
 134
 135   protected JCheckBox identity = new JCheckBox();
 136
 137   protected JCheckBox showGroupConsensus = new JCheckBox();
 138
 139   protected JCheckBox showGroupConservation = new JCheckBox();
 140
 141   protected JCheckBox showConsensHistogram = new JCheckBox();
 142
 143   protected JCheckBox showConsensLogo = new JCheckBox();
 144
 145   protected JCheckBox showDbRefTooltip = new JCheckBox();
 146
 147   protected JCheckBox showNpTooltip = new JCheckBox();
 148
 149   /*
 150    * Structure tab and components
 151    */
 152   protected JPanel structureTab;
 153
 154   protected JCheckBox structFromPdb = new JCheckBox();
 155
 156   protected JCheckBox useRnaView = new JCheckBox();
 157
 158   protected JCheckBox addSecondaryStructure = new JCheckBox();
 159
 160   protected JCheckBox addTempFactor = new JCheckBox();
 161
 162   protected JComboBox<String> structViewer = new JComboBox<String>();
 163
 164   protected JTextField chimeraPath = new JTextField();
 165
 166   protected ButtonGroup mappingMethod = new ButtonGroup();
 167
 168   protected JRadioButton siftsMapping = new JRadioButton();
 169
 170   protected JRadioButton nwMapping = new JRadioButton();
 171
 172   /*
 173    * Colours tab components
 174    */
 175   protected JPanel minColour = new JPanel();
 176
 177   protected JPanel maxColour = new JPanel();
 178
 179   protected JComboBox<String> protColour = new JComboBox<String>();
 180
 181   protected JComboBox<String> nucColour = new JComboBox<String>();
 182
 183   /*
 184    * Connections tab components
 185    */
 186   protected JTable linkUrlTable = new JTable();
 187
 188   protected JButton editLink = new JButton();
 189
 190   protected JButton deleteLink = new JButton();
 191
 192   protected JTextField filterTB = new JTextField();
 193
 194   protected JButton doReset = new JButton();
 195
 196   protected JButton userOnly = new JButton();
 197
 198   protected JLabel portLabel = new JLabel();
 199
 200   protected JLabel serverLabel = new JLabel();
 201
 202   protected JTextField proxyServerTB = new JTextField();
 203
 204   protected JTextField proxyPortTB = new JTextField();
 205
 206   protected JTextField defaultBrowser = new JTextField();
 207
 208   protected JCheckBox useProxy = new JCheckBox();
 209
 210   protected JCheckBox usagestats = new JCheckBox();
 211
 212   protected JCheckBox questionnaire = new JCheckBox();
 213
 214   protected JCheckBox versioncheck = new JCheckBox();
 215
 216   /*
 217    * Output tab components
 218    */
 219   protected JComboBox<Object> epsRendering = new JComboBox<Object>();
 220
 221   protected JLabel userIdWidthlabel = new JLabel();
 222
 223   protected JCheckBox autoIdWidth = new JCheckBox();
 224
 225   protected JTextField userIdWidth = new JTextField();
 226
 227   protected JCheckBox blcjv = new JCheckBox();
 228
 229   protected JCheckBox pileupjv = new JCheckBox();
 230
 231   protected JCheckBox clustaljv = new JCheckBox();
 232
 233   protected JCheckBox msfjv = new JCheckBox();
 234
 235   protected JCheckBox fastajv = new JCheckBox();
 236
 237   protected JCheckBox pfamjv = new JCheckBox();
 238
 239   protected JCheckBox pirjv = new JCheckBox();
 240
 241   protected JCheckBox modellerOutput = new JCheckBox();
 242
 243   protected JCheckBox embbedBioJSON = new JCheckBox();
 244
 245   /*
 246    * Editing tab components
 247    */
 248   protected JCheckBox autoCalculateConsCheck = new JCheckBox();
 249
 250   protected JCheckBox padGaps = new JCheckBox();
 251
 252   protected JCheckBox sortByTree = new JCheckBox();
 253
 254   /*
 255    * DAS Settings tab
 256    */
 257   protected JPanel dasTab = new JPanel();
 258
 259   /*
 260    * Web Services tab
 261    */
 262   protected JPanel wsTab = new JPanel();
 263
 264   /**
 265    * Creates a new GPreferences object.
 266    */
 267   public GPreferences()
 268   {
 269     try
 270     {
 271       jbInit();
 272     } catch (Exception ex)
 273     {
 274       ex.printStackTrace();
 275     }
 276   }
 277
 278   /**
 279    * Construct the panel and its tabbed sub-panels.
 280    *
 281    * @throws Exception
 282    */
 283   private void jbInit() throws Exception
 284   {
 285     final JTabbedPane tabbedPane = new JTabbedPane();
 286     this.setLayout(new BorderLayout());
 287     JPanel okCancelPanel = initOkCancelPanel();
 288     this.add(tabbedPane, BorderLayout.CENTER);
 289     this.add(okCancelPanel, BorderLayout.SOUTH);
 290
 291     tabbedPane.add(initVisualTab(),
 292             MessageManager.getString("label.visual"));
 293
 294     tabbedPane.add(initColoursTab(),
 295             MessageManager.getString("label.colours"));
 296
 297     tabbedPane.add(initStructureTab(),
 298             MessageManager.getString("label.structure"));
 299
 300     tabbedPane.add(initConnectionsTab(),
 301             MessageManager.getString("label.connections"));
 302
 303     tabbedPane.add(initLinksTab(),
 304             MessageManager.getString("label.urllinks"));
 305
 306     tabbedPane.add(initOutputTab(),
 307             MessageManager.getString("label.output"));
 308
 309     tabbedPane.add(initEditingTab(),
 310             MessageManager.getString("label.editing"));
 311
 312     /*
 313      * See DasSourceBrowser for the real work of configuring this tab.
 314      */
 315     dasTab.setLayout(new BorderLayout());
 316     tabbedPane.add(dasTab, MessageManager.getString("label.das_settings"));
 317
 318     /*
 319      * See WsPreferences for the real work of configuring this tab.
 320      */
 321     wsTab.setLayout(new BorderLayout());
 322     tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
 323
 324     /*
 325      * Handler to validate a tab before leaving it - currently only for
 326      * Structure.
 327      */
 328     tabbedPane.addChangeListener(new ChangeListener()
 329     {
 330       private Component lastTab;
 331
 332       @Override
 333       public void stateChanged(ChangeEvent e)
 334       {
 335         if (lastTab == structureTab
 336                 && tabbedPane.getSelectedComponent() != structureTab)
 337         {
 338           if (!validateStructure())
 339           {
 340             tabbedPane.setSelectedComponent(structureTab);
 341             return;
 342           }
 343         }
 344         lastTab = tabbedPane.getSelectedComponent();
 345       }
 346
 347     });
 348   }
 349
 350   /**
 351    * Initialises the Editing tabbed panel.
 352    *
 353    * @return
 354    */
 355   private JPanel initEditingTab()
 356   {
 357     JPanel editingTab = new JPanel();
 358     editingTab.setLayout(null);
 359     autoCalculateConsCheck.setFont(LABEL_FONT);
 360     autoCalculateConsCheck.setText(MessageManager
 361             .getString("label.autocalculate_consensus"));
 362     autoCalculateConsCheck.setBounds(new Rectangle(21, 52, 209, 23));
 363     padGaps.setFont(LABEL_FONT);
 364     padGaps.setText(MessageManager.getString("label.pad_gaps_when_editing"));
 365     padGaps.setBounds(new Rectangle(22, 94, 168, 23));
 366     sortByTree.setFont(LABEL_FONT);
 367     sortByTree
 368             .setText(MessageManager.getString("label.sort_with_new_tree"));
 369     sortByTree
 370             .setToolTipText(MessageManager
 371                     .getString("label.any_trees_calculated_or_loaded_alignment_automatically_sort"));
 372     sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
 373     editingTab.add(autoCalculateConsCheck);
 374     editingTab.add(padGaps);
 375     editingTab.add(sortByTree);
 376     return editingTab;
 377   }
 378
 379   /**
 380    * Initialises the Output tabbed panel.
 381    *
 382    * @return
 383    */
 384   private JPanel initOutputTab()
 385   {
 386     JPanel outputTab = new JPanel();
 387     outputTab.setLayout(null);
 388     JLabel epsLabel = new JLabel();
 389     epsLabel.setFont(LABEL_FONT);
 390     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 391     epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
 392     epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
 393     epsRendering.setFont(LABEL_FONT);
 394     epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
 395     JLabel jLabel1 = new JLabel();
 396     jLabel1.setFont(LABEL_FONT);
 397     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
 398     jLabel1.setText(MessageManager.getString("label.append_start_end"));
 399     jLabel1.setFont(LABEL_FONT);
 400     fastajv.setFont(LABEL_FONT);
 401     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
 402     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
 403     blcjv.setText(MessageManager.getString("label.blc") + "     ");
 404     fastajv.setText(MessageManager.getString("label.fasta") + "     ");
 405     msfjv.setText(MessageManager.getString("label.msf") + "     ");
 406     pfamjv.setText(MessageManager.getString("label.pfam") + "     ");
 407     pileupjv.setText(MessageManager.getString("label.pileup") + "     ");
 408     msfjv.setFont(LABEL_FONT);
 409     msfjv.setHorizontalAlignment(SwingConstants.LEFT);
 410     pirjv.setText(MessageManager.getString("label.pir") + "     ");
 411     JPanel jPanel11 = new JPanel();
 412     jPanel11.setFont(LABEL_FONT);
 413     TitledBorder titledBorder2 = new TitledBorder(
 414             MessageManager.getString("label.file_output"));
 415     jPanel11.setBorder(titledBorder2);
 416     jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
 417     GridLayout gridLayout3 = new GridLayout();
 418     jPanel11.setLayout(gridLayout3);
 419     gridLayout3.setRows(8);
 420     blcjv.setFont(LABEL_FONT);
 421     blcjv.setHorizontalAlignment(SwingConstants.LEFT);
 422     clustaljv.setFont(LABEL_FONT);
 423     clustaljv.setHorizontalAlignment(SwingConstants.LEFT);
 424     pfamjv.setFont(LABEL_FONT);
 425     pfamjv.setHorizontalAlignment(SwingConstants.LEFT);
 426     pileupjv.setFont(LABEL_FONT);
 427     pileupjv.setHorizontalAlignment(SwingConstants.LEFT);
 428     pirjv.setFont(LABEL_FONT);
 429     pirjv.setHorizontalAlignment(SwingConstants.LEFT);
 430     autoIdWidth.setFont(LABEL_FONT);
 431     autoIdWidth.setText(MessageManager
 432             .getString("label.automatically_set_id_width"));
 433     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true,
 434             MessageManager
 435                     .getString("label.adjusts_width_generated_eps_png")));
 436     autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
 437     autoIdWidth.addActionListener(new ActionListener()
 438     {
 439
 440       @Override
 441       public void actionPerformed(ActionEvent e)
 442       {
 443         autoIdWidth_actionPerformed();
 444       }
 445     });
 446     userIdWidthlabel.setFont(LABEL_FONT);
 447     userIdWidthlabel.setText(MessageManager
 448             .getString("label.figure_id_column_width"));
 449     userIdWidth
 450             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 451                     .getString("label.manually_specify_width_left_column")));
 452     userIdWidthlabel
 453             .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
 454                     .getString("label.manually_specify_width_left_column")));
 455     userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
 456     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
 457     userIdWidth.setText("");
 458     userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
 459     userIdWidth.addActionListener(new ActionListener()
 460     {
 461
 462       @Override
 463       public void actionPerformed(ActionEvent e)
 464       {
 465         userIdWidth_actionPerformed();
 466       }
 467     });
 468     modellerOutput.setFont(LABEL_FONT);
 469     modellerOutput.setText(MessageManager
 470             .getString("label.use_modeller_output"));
 471     modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
 472     embbedBioJSON.setFont(LABEL_FONT);
 473     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
 474     embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
 475
 476     jPanel11.add(jLabel1);
 477     jPanel11.add(blcjv);
 478     jPanel11.add(clustaljv);
 479     jPanel11.add(fastajv);
 480     jPanel11.add(msfjv);
 481     jPanel11.add(pfamjv);
 482     jPanel11.add(pileupjv);
 483     jPanel11.add(pirjv);
 484     outputTab.add(autoIdWidth);
 485     outputTab.add(userIdWidth);
 486     outputTab.add(userIdWidthlabel);
 487     outputTab.add(modellerOutput);
 488     outputTab.add(embbedBioJSON);
 489     outputTab.add(epsLabel);
 490     outputTab.add(epsRendering);
 491     outputTab.add(jPanel11);
 492     return outputTab;
 493   }
 494
 495   /**
 496    * Initialises the Connections tabbed panel.
 497    *
 498    * @return
 499    */
 500   private JPanel initConnectionsTab()
 501   {
 502     JPanel connectTab = new JPanel();
 503     connectTab.setLayout(new GridBagLayout());
 504
 505     // Label for browser text box
 506     JLabel browserLabel = new JLabel();
 507     browserLabel.setFont(LABEL_FONT);
 508     browserLabel.setHorizontalAlignment(SwingConstants.TRAILING);
 509     browserLabel.setText(MessageManager
 510             .getString("label.default_browser_unix"));
 511     defaultBrowser.setFont(LABEL_FONT);
 512     defaultBrowser.setText("");
 513
 514     defaultBrowser.addMouseListener(new MouseAdapter()
 515     {
 516       @Override
 517       public void mouseClicked(MouseEvent e)
 518       {
 519         if (e.getClickCount() > 1)
 520         {
 521           defaultBrowser_mouseClicked(e);
 522         }
 523       }
 524     });
 525
 526     JPanel proxyPanel = initConnTabProxyPanel();
 527     initConnTabCheckboxes();
 528
 529     // Add default Browser text box
 530     connectTab.add(browserLabel, new GridBagConstraints(0, 0, 1, 1, 0.0,
 531             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 532             new Insets(10, 0, 5, 5), 5, 1));
 533     defaultBrowser.setFont(LABEL_FONT);
 534     defaultBrowser.setText("");
 535
 536     connectTab.add(defaultBrowser, new GridBagConstraints(1, 0, 1, 1, 1.0,
 537             0.0, GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 538             new Insets(10, 0, 5, 10), 30, 1));
 539
 540     // Add proxy server panel
 541     connectTab.add(proxyPanel, new GridBagConstraints(0, 1, 2, 1, 1.0, 0.0,
 542             GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL,
 543             new Insets(10, 0, 5, 12), 4, 10));
 544
 545     // Add usage stats, version check and questionnaire checkboxes
 546     connectTab.add(usagestats, new GridBagConstraints(0, 2, 1, 1, 1.0, 0.0,
 547             GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 548             new Insets(0, 2, 5, 5), 70, 1));
 549     connectTab.add(questionnaire, new GridBagConstraints(1, 2, 1, 1, 1.0,
 550             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 551             new Insets(0, 2, 5, 10), 70, 1));
 552     connectTab.add(versioncheck, new GridBagConstraints(0, 3, 1, 1, 1.0,
 553             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 554             new Insets(0, 2, 5, 5), 70, 1));
 555
 556     // Add padding so the panel doesn't look ridiculous
 557     JPanel spacePanel = new JPanel();
 558     connectTab.add(spacePanel, new GridBagConstraints(0, 4, 1, 1, 1.0, 1.0,
 559             GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets(0,
 560                     0, 0, 5), 70, 1));
 561
 562     return connectTab;
 563   }
 564
 565   /**
 566    * Initialises the Links tabbed panel.
 567    *
 568    * @return
 569    */
 570   private JPanel initLinksTab()
 571   {
 572     JPanel linkTab = new JPanel();
 573     linkTab.setLayout(new GridBagLayout());
 574
 575     // Set up table for Url links
 576     linkUrlTable.setFillsViewportHeight(true);
 577     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
 578     linkUrlTable.setAutoCreateRowSorter(true);
 579     linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
 580
 581     // adjust row height so radio buttons actually fit
 582     // don't do this in the renderer, it causes the awt thread to activate
 583     // constantly
 584     JRadioButton temp = new JRadioButton();
 585     linkUrlTable.setRowHeight(temp.getMinimumSize().height);
 586
 587     // Table in scrollpane so that the table is given a scrollbar
 588     JScrollPane linkScrollPane = new JScrollPane(linkUrlTable);
 589     linkScrollPane.setBorder(null);
 590
 591     // Panel for links functionality
 592     JPanel linkPanel = new JPanel(new GridBagLayout());
 593     linkPanel.setBorder(new TitledBorder(MessageManager
 594             .getString("label.url_linkfrom_sequence_id")));
 595
 596     // Put the Url links panel together
 597
 598     // Buttons go at top right, resizing only resizes the blank space vertically
 599     JPanel buttonPanel = initLinkTabUrlButtons();
 600     GridBagConstraints linkConstraints1 = new GridBagConstraints();
 601     linkConstraints1.insets = new Insets(0, 0, 5, 0);
 602     linkConstraints1.gridx = 0;
 603     linkConstraints1.gridy = 0;
 604     linkConstraints1.weightx = 1.0;
 605     linkConstraints1.fill = GridBagConstraints.HORIZONTAL;
 606     linkTab.add(buttonPanel, linkConstraints1);
 607
 608     // Links table goes at top left, resizing resizes the table
 609     GridBagConstraints linkConstraints2 = new GridBagConstraints();
 610     linkConstraints2.insets = new Insets(0, 0, 5, 5);
 611     linkConstraints2.gridx = 0;
 612     linkConstraints2.gridy = 1;
 613     linkConstraints2.weightx = 1.0;
 614     linkConstraints2.weighty = 1.0;
 615     linkConstraints2.fill = GridBagConstraints.BOTH;
 616     linkTab.add(linkScrollPane, linkConstraints2);
 617
 618     // Filter box and buttons goes at bottom left, resizing resizes the text box
 619     JPanel filterPanel = initLinkTabFilterPanel();
 620     GridBagConstraints linkConstraints3 = new GridBagConstraints();
 621     linkConstraints3.insets = new Insets(0, 0, 0, 5);
 622     linkConstraints3.gridx = 0;
 623     linkConstraints3.gridy = 2;
 624     linkConstraints3.weightx = 1.0;
 625     linkConstraints3.fill = GridBagConstraints.HORIZONTAL;
 626     linkTab.add(filterPanel, linkConstraints3);
 627
 628     return linkTab;
 629   }
 630
 631   private JPanel initLinkTabFilterPanel()
 632   {
 633     // Filter textbox and reset button
 634     JLabel filterLabel = new JLabel(
 635             MessageManager.getString("label.filter"));
 636     filterLabel.setFont(LABEL_FONT);
 637     filterLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 638     filterLabel.setHorizontalTextPosition(SwingConstants.LEADING);
 639
 640     filterTB.setFont(LABEL_FONT);
 641     filterTB.setText("");
 642
 643     doReset.setText(MessageManager.getString("action.showall"));
 644     userOnly.setText(MessageManager.getString("action.customfilter"));
 645
 646     // Panel for filter functionality
 647     JPanel filterPanel = new JPanel(new GridBagLayout());
 648     filterPanel.setBorder(new TitledBorder("Filter"));
 649     GridBagConstraints gbc = new GridBagConstraints();
 650     gbc.gridx = 0;
 651     gbc.gridy = 0;
 652     gbc.fill = GridBagConstraints.NONE;
 653     gbc.anchor = GridBagConstraints.WEST;
 654
 655     filterPanel.add(filterLabel, gbc);
 656
 657     GridBagConstraints gbc1 = new GridBagConstraints();
 658     gbc1.gridx = 1;
 659     gbc1.gridwidth = 2;
 660     gbc1.fill = GridBagConstraints.HORIZONTAL;
 661     gbc1.anchor = GridBagConstraints.WEST;
 662     gbc1.weightx = 1.0;
 663     filterPanel.add(filterTB, gbc1);
 664
 665     GridBagConstraints gbc2 = new GridBagConstraints();
 666     gbc2.gridx = 3;
 667     gbc2.fill = GridBagConstraints.NONE;
 668     gbc2.anchor = GridBagConstraints.WEST;
 669     filterPanel.add(doReset, gbc2);
 670
 671     GridBagConstraints gbc3 = new GridBagConstraints();
 672     gbc3.gridx = 4;
 673     gbc3.fill = GridBagConstraints.NONE;
 674     gbc3.anchor = GridBagConstraints.WEST;
 675     filterPanel.add(userOnly, gbc3);
 676
 677     return filterPanel;
 678   }
 679
 680   private JPanel initLinkTabUrlButtons()
 681   {
 682     // Buttons for new / edit / delete Url links
 683     JButton newLink = new JButton();
 684     newLink.setText(MessageManager.getString("action.new"));
 685
 686     editLink.setText(MessageManager.getString("action.edit"));
 687
 688     deleteLink.setText(MessageManager.getString("action.delete"));
 689
 690     // no current selection, so initially disable delete/edit buttons
 691     editLink.setEnabled(false);
 692     deleteLink.setEnabled(false);
 693
 694     newLink.addActionListener(new java.awt.event.ActionListener()
 695     {
 696       @Override
 697       public void actionPerformed(ActionEvent e)
 698       {
 699         newLink_actionPerformed(e);
 700       }
 701     });
 702
 703     editLink.setText(MessageManager.getString("action.edit"));
 704     editLink.addActionListener(new java.awt.event.ActionListener()
 705     {
 706       @Override
 707       public void actionPerformed(ActionEvent e)
 708       {
 709         editLink_actionPerformed(e);
 710       }
 711     });
 712
 713     deleteLink.setText(MessageManager.getString("action.delete"));
 714     deleteLink.addActionListener(new java.awt.event.ActionListener()
 715     {
 716       @Override
 717       public void actionPerformed(ActionEvent e)
 718       {
 719         deleteLink_actionPerformed(e);
 720       }
 721     });
 722
 723     JPanel buttonPanel = new JPanel(new GridBagLayout());
 724     buttonPanel.setBorder(new TitledBorder("Edit links"));
 725     GridBagConstraints gbc = new GridBagConstraints();
 726     gbc.gridx = 0;
 727     gbc.gridy = 0;
 728     gbc.fill = GridBagConstraints.NONE;
 729     buttonPanel.add(newLink, gbc);
 730
 731     GridBagConstraints gbc1 = new GridBagConstraints();
 732     gbc1.gridx = 1;
 733     gbc1.gridy = 0;
 734     gbc1.fill = GridBagConstraints.NONE;
 735     buttonPanel.add(editLink, gbc1);
 736
 737     GridBagConstraints gbc2 = new GridBagConstraints();
 738     gbc2.gridx = 2;
 739     gbc2.gridy = 0;
 740     gbc2.fill = GridBagConstraints.NONE;
 741     buttonPanel.add(deleteLink, gbc2);
 742
 743     GridBagConstraints gbc3 = new GridBagConstraints();
 744     gbc3.gridx = 3;
 745     gbc3.gridy = 0;
 746     gbc3.fill = GridBagConstraints.HORIZONTAL;
 747     gbc3.weightx = 1.0;
 748     JPanel spacePanel = new JPanel();
 749     spacePanel.setBorder(null);
 750     buttonPanel.add(spacePanel, gbc3);
 751
 752     return buttonPanel;
 753   }
 754
 755   /**
 756    * Initialises the proxy server panel in the Connections tab
 757    *
 758    * @return the proxy server panel
 759    */
 760   private JPanel initConnTabProxyPanel()
 761   {
 762     // Label for server text box
 763     serverLabel.setText(MessageManager.getString("label.address"));
 764     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 765     serverLabel.setFont(LABEL_FONT);
 766
 767     // Proxy server and port text boxes
 768     proxyServerTB.setFont(LABEL_FONT);
 769     proxyPortTB.setFont(LABEL_FONT);
 770
 771     // Label for Port text box
 772     portLabel.setFont(LABEL_FONT);
 773     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 774     portLabel.setText(MessageManager.getString("label.port"));
 775
 776     // Use proxy server checkbox
 777     useProxy.setFont(LABEL_FONT);
 778     useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
 779     useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
 780     useProxy.setText(MessageManager.getString("label.use_proxy_server"));
 781     useProxy.addActionListener(new ActionListener()
 782     {
 783       @Override
 784       public void actionPerformed(ActionEvent e)
 785       {
 786         useProxy_actionPerformed();
 787       }
 788     });
 789
 790     // Make proxy server panel
 791     JPanel proxyPanel = new JPanel();
 792     TitledBorder titledBorder1 = new TitledBorder(
 793             MessageManager.getString("label.proxy_server"));
 794     proxyPanel.setBorder(titledBorder1);
 795     proxyPanel.setLayout(new GridBagLayout());
 796     proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0,
 797             0.0, GridBagConstraints.WEST, GridBagConstraints.NONE,
 798             new Insets(0, 2, 2, 0), 5, 0));
 799     proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
 800             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 801                     0, 2, 0), 11, 0));
 802     proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
 803             GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0,
 804                     2, 5, 185), 2, -4));
 805     proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0,
 806             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 807             new Insets(0, 2, 2, 2), 54, 1));
 808     proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0,
 809             0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
 810             new Insets(0, 2, 2, 0), 263, 1));
 811
 812     return proxyPanel;
 813   }
 814
 815   /**
 816    * Initialises the checkboxes in the Connections tab
 817    */
 818   private void initConnTabCheckboxes()
 819   {
 820     // Usage stats checkbox label
 821     usagestats.setText(MessageManager
 822             .getString("label.send_usage_statistics"));
 823     usagestats.setFont(LABEL_FONT);
 824     usagestats.setHorizontalAlignment(SwingConstants.RIGHT);
 825     usagestats.setHorizontalTextPosition(SwingConstants.LEADING);
 826
 827     // Questionnaire checkbox label
 828     questionnaire.setText(MessageManager
 829             .getString("label.check_for_questionnaires"));
 830     questionnaire.setFont(LABEL_FONT);
 831     questionnaire.setHorizontalAlignment(SwingConstants.RIGHT);
 832     questionnaire.setHorizontalTextPosition(SwingConstants.LEADING);
 833
 834     // Check for latest version checkbox label
 835     versioncheck.setText(MessageManager
 836             .getString("label.check_for_latest_version"));
 837     versioncheck.setFont(LABEL_FONT);
 838     versioncheck.setHorizontalAlignment(SwingConstants.RIGHT);
 839     versioncheck.setHorizontalTextPosition(SwingConstants.LEADING);
 840   }
 841
 842   /**
 843    * Initialises the parent panel which contains the tabbed sections.
 844    *
 845    * @return
 846    */
 847   private JPanel initOkCancelPanel()
 848   {
 849     JButton ok = new JButton();
 850     ok.setText(MessageManager.getString("action.ok"));
 851     ok.addActionListener(new ActionListener()
 852     {
 853       @Override
 854       public void actionPerformed(ActionEvent e)
 855       {
 856         ok_actionPerformed(e);
 857       }
 858     });
 859     JButton cancel = new JButton();
 860     cancel.setText(MessageManager.getString("action.cancel"));
 861     cancel.addActionListener(new ActionListener()
 862     {
 863       @Override
 864       public void actionPerformed(ActionEvent e)
 865       {
 866         cancel_actionPerformed(e);
 867       }
 868     });
 869     JPanel okCancelPanel = new JPanel();
 870     okCancelPanel.add(ok);
 871     okCancelPanel.add(cancel);
 872     return okCancelPanel;
 873   }
 874
 875   /**
 876    * Initialises the Colours tabbed panel.
 877    *
 878    * @return
 879    */
 880   private JPanel initColoursTab()
 881   {
 882     JPanel coloursTab = new JPanel();
 883     coloursTab.setBorder(new TitledBorder(MessageManager
 884             .getString("action.open_new_alignment")));
 885     coloursTab.setLayout(new FlowLayout());
 886     JLabel mincolourLabel = new JLabel();
 887     mincolourLabel.setFont(LABEL_FONT);
 888     mincolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 889     mincolourLabel.setText(MessageManager.getString("label.min_colour"));
 890     minColour.setFont(LABEL_FONT);
 891     minColour.setBorder(BorderFactory.createEtchedBorder());
 892     minColour.setPreferredSize(new Dimension(40, 20));
 893     minColour.addMouseListener(new MouseAdapter()
 894     {
 895       @Override
 896       public void mousePressed(MouseEvent e)
 897       {
 898         minColour_actionPerformed(minColour);
 899       }
 900     });
 901     JLabel maxcolourLabel = new JLabel();
 902     maxcolourLabel.setFont(LABEL_FONT);
 903     maxcolourLabel.setHorizontalAlignment(SwingConstants.RIGHT);
 904     maxcolourLabel.setText(MessageManager.getString("label.max_colour"));
 905     maxColour.setFont(LABEL_FONT);
 906     maxColour.setBorder(BorderFactory.createEtchedBorder());
 907     maxColour.setPreferredSize(new Dimension(40, 20));
 908     maxColour.addMouseListener(new MouseAdapter()
 909     {
 910       @Override
 911       public void mousePressed(MouseEvent e)
 912       {
 913         maxColour_actionPerformed(maxColour);
 914       }
 915     });
 916
 917     protColour.setFont(LABEL_FONT);
 918     protColour.setBounds(new Rectangle(172, 225, 155, 21));
 919     JLabel protColourLabel = new JLabel();
 920     protColourLabel.setFont(LABEL_FONT);
 921     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 922     protColourLabel.setText(MessageManager
 923             .getString("label.prot_alignment_colour") + " ");
 924     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 925             .getString("label.default_colour_scheme_for_alignment"),
 926             protColourLabel, protColour);
 927
 928     nucColour.setFont(LABEL_FONT);
 929     nucColour.setBounds(new Rectangle(172, 240, 155, 21));
 930     JLabel nucColourLabel = new JLabel();
 931     nucColourLabel.setFont(LABEL_FONT);
 932     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
 933     nucColourLabel.setText(MessageManager
 934             .getString("label.nuc_alignment_colour") + " ");
 935     JvSwingUtils.addtoLayout(coloursTab, MessageManager
 936             .getString("label.default_colour_scheme_for_alignment"),
 937             nucColourLabel, nucColour);
 938
 939     JPanel annotationShding = new JPanel();
 940     annotationShding.setBorder(new TitledBorder(MessageManager
 941             .getString("label.annotation_shading_default")));
 942     annotationShding.setLayout(new GridLayout(1, 2));
 943     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 944             .getString("label.default_minimum_colour_annotation_shading"),
 945             mincolourLabel, minColour);
 946     JvSwingUtils.addtoLayout(annotationShding, MessageManager
 947             .getString("label.default_maximum_colour_annotation_shading"),
 948             maxcolourLabel, maxColour);
 949     coloursTab.add(annotationShding); // , FlowLayout.LEFT);
 950     return coloursTab;
 951   }
 952
 953   /**
 954    * Initialises the Structure tabbed panel.
 955    *
 956    * @return
 957    */
 958   private JPanel initStructureTab()
 959   {
 960     structureTab = new JPanel();
 961
 962     structureTab.setBorder(new TitledBorder(MessageManager
 963             .getString("label.structure_options")));
 964     structureTab.setLayout(null);
 965     final int width = 400;
 966     final int height = 22;
 967     final int lineSpacing = 25;
 968     int ypos = 15;
 969
 970     structFromPdb.setFont(LABEL_FONT);
 971     structFromPdb
 972             .setText(MessageManager.getString("label.struct_from_pdb"));
 973     structFromPdb.setBounds(new Rectangle(5, ypos, width, height));
 974     structFromPdb.addActionListener(new ActionListener()
 975     {
 976       @Override
 977       public void actionPerformed(ActionEvent e)
 978       {
 979         boolean selected = structFromPdb.isSelected();
 980         // enable other options only when the first is checked
 981         useRnaView.setEnabled(selected);
 982         addSecondaryStructure.setEnabled(selected);
 983         addTempFactor.setEnabled(selected);
 984       }
 985     });
 986     structureTab.add(structFromPdb);
 987
 988     // indent checkboxes that are conditional on the first one
 989     ypos += lineSpacing;
 990     useRnaView.setFont(LABEL_FONT);
 991     useRnaView.setText(MessageManager.getString("label.use_rnaview"));
 992     useRnaView.setBounds(new Rectangle(25, ypos, width, height));
 993     structureTab.add(useRnaView);
 994
 995     ypos += lineSpacing;
 996     addSecondaryStructure.setFont(LABEL_FONT);
 997     addSecondaryStructure.setText(MessageManager
 998             .getString("label.autoadd_secstr"));
 999     addSecondaryStructure.setBounds(new Rectangle(25, ypos, width, height));
1000     structureTab.add(addSecondaryStructure);
1001
1002     ypos += lineSpacing;
1003     addTempFactor.setFont(LABEL_FONT);
1004     addTempFactor.setText(MessageManager.getString("label.autoadd_temp"));
1005     addTempFactor.setBounds(new Rectangle(25, ypos, width, height));
1006     structureTab.add(addTempFactor);
1007
1008     ypos += lineSpacing;
1009     JLabel viewerLabel = new JLabel();
1010     viewerLabel.setFont(LABEL_FONT);
1011     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
1012     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
1013     viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
1014     structureTab.add(viewerLabel);
1015
1016     structViewer.setFont(LABEL_FONT);
1017     structViewer.setBounds(new Rectangle(160, ypos, 120, height));
1018     structViewer.addItem(ViewerType.JMOL.name());
1019     structViewer.addItem(ViewerType.CHIMERA.name());
1020     structViewer.addActionListener(new ActionListener()
1021     {
1022       @Override
1023       public void actionPerformed(ActionEvent e)
1024       {
1025         structureViewer_actionPerformed((String) structViewer
1026                 .getSelectedItem());
1027       }
1028     });
1029     structureTab.add(structViewer);
1030
1031     ypos += lineSpacing;
1032     JLabel pathLabel = new JLabel();
1033     pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
1034     pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
1035     pathLabel.setText(MessageManager.getString("label.chimera_path"));
1036     final String tooltip = JvSwingUtils.wrapTooltip(true,
1037             MessageManager.getString("label.chimera_path_tip"));
1038     pathLabel.setToolTipText(tooltip);
1039     pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
1040     structureTab.add(pathLabel);
1041
1042     chimeraPath.setFont(LABEL_FONT);
1043     chimeraPath.setText("");
1044     chimeraPath.setBounds(new Rectangle(160, ypos, 300, height));
1045     chimeraPath.addMouseListener(new MouseAdapter()
1046     {
1047       @Override
1048       public void mouseClicked(MouseEvent e)
1049       {
1050         if (e.getClickCount() == 2)
1051         {
1052           String chosen = openFileChooser();
1053           if (chosen != null)
1054           {
1055             chimeraPath.setText(chosen);
1056           }
1057         }
1058       }
1059     });
1060     structureTab.add(chimeraPath);
1061
1062     ypos += lineSpacing;
1063     nwMapping.setFont(LABEL_FONT);
1064     nwMapping.setText(MessageManager.getString("label.nw_mapping"));
1065     siftsMapping.setFont(LABEL_FONT);
1066     siftsMapping.setText(MessageManager.getString("label.sifts_mapping"));
1067     mappingMethod.add(nwMapping);
1068     mappingMethod.add(siftsMapping);
1069     JPanel mappingPanel = new JPanel();
1070     mappingPanel.setFont(LABEL_FONT);
1071     TitledBorder mmTitledBorder = new TitledBorder(
1072             MessageManager.getString("label.mapping_method"));
1073     mmTitledBorder.setTitleFont(LABEL_FONT);
1074     mappingPanel.setBorder(mmTitledBorder);
1075     mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
1076     // GridLayout mappingLayout = new GridLayout();
1077     mappingPanel.setLayout(new GridLayout());
1078     mappingPanel.add(nwMapping);
1079     mappingPanel.add(siftsMapping);
1080     structureTab.add(mappingPanel);
1081
1082     ypos += lineSpacing;
1083     ypos += lineSpacing;
1084     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
1085             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
1086     docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
1087     structureTab.add(docFieldPref);
1088
1089     return structureTab;
1090   }
1091
1092   /**
1093    * Action on choosing a structure viewer from combobox options.
1094    *
1095    * @param selectedItem
1096    */
1097   protected void structureViewer_actionPerformed(String selectedItem)
1098   {
1099   }
1100
1101   /**
1102    * Show a dialog for the user to choose a file. Returns the chosen path, or
1103    * null on Cancel.
1104    *
1105    * @return
1106    */
1107   protected String openFileChooser()
1108   {
1109     String choice = null;
1110     JFileChooser chooser = new JFileChooser();
1111
1112     // chooser.setFileView(new JalviewFileView());
1113     chooser.setDialogTitle(MessageManager
1114             .getString("label.open_local_file"));
1115     chooser.setToolTipText(MessageManager.getString("action.open"));
1116
1117     int value = chooser.showOpenDialog(this);
1118
1119     if (value == JFileChooser.APPROVE_OPTION)
1120     {
1121       choice = chooser.getSelectedFile().getPath();
1122     }
1123     return choice;
1124   }
1125
1126   /**
1127    * Validate the structure tab preferences; if invalid, set focus on this tab.
1128    *
1129    * @param e
1130    */
1131   protected boolean validateStructure(FocusEvent e)
1132   {
1133     if (!validateStructure())
1134     {
1135       e.getComponent().requestFocusInWindow();
1136       return false;
1137     }
1138     return true;
1139   }
1140
1141   protected boolean validateStructure()
1142   {
1143     return false;
1144   }
1145
1146   /**
1147    * Initialises the Visual tabbed panel.
1148    *
1149    * @return
1150    */
1151   private JPanel initVisualTab()
1152   {
1153     JPanel visualTab = new JPanel();
1154     visualTab.setBorder(new TitledBorder(MessageManager
1155             .getString("action.open_new_alignment")));
1156     visualTab.setLayout(null);
1157     fullScreen.setFont(LABEL_FONT);
1158     fullScreen.setHorizontalAlignment(SwingConstants.RIGHT);
1159     fullScreen.setHorizontalTextPosition(SwingConstants.LEFT);
1160     fullScreen.setText(MessageManager.getString("label.maximize_window"));
1161     quality.setEnabled(false);
1162     quality.setFont(LABEL_FONT);
1163     quality.setHorizontalAlignment(SwingConstants.RIGHT);
1164     quality.setHorizontalTextPosition(SwingConstants.LEFT);
1165     quality.setSelected(true);
1166     quality.setText(MessageManager.getString("label.quality"));
1167     conservation.setEnabled(false);
1168     conservation.setFont(LABEL_FONT);
1169     conservation.setHorizontalAlignment(SwingConstants.RIGHT);
1170     conservation.setHorizontalTextPosition(SwingConstants.LEFT);
1171     conservation.setSelected(true);
1172     conservation.setText(MessageManager.getString("label.conservation"));
1173     identity.setEnabled(false);
1174     identity.setFont(LABEL_FONT);
1175     identity.setHorizontalAlignment(SwingConstants.RIGHT);
1176     identity.setHorizontalTextPosition(SwingConstants.LEFT);
1177     identity.setSelected(true);
1178     identity.setText(MessageManager.getString("label.consensus"));
1179     showOccupancy.setFont(LABEL_FONT);
1180     showOccupancy.setEnabled(false);
1181     showOccupancy.setHorizontalAlignment(SwingConstants.RIGHT);
1182     showOccupancy.setHorizontalTextPosition(SwingConstants.LEFT);
1183     showOccupancy.setSelected(true);
1184     showOccupancy.setText(MessageManager.getString("label.occupancy"));
1185
1186     JLabel showGroupbits = new JLabel();
1187     showGroupbits.setFont(LABEL_FONT);
1188     showGroupbits.setHorizontalAlignment(SwingConstants.RIGHT);
1189     showGroupbits.setHorizontalTextPosition(SwingConstants.LEFT);
1190     showGroupbits.setText(MessageManager.getString("action.show_group")
1191             + ":");
1192     JLabel showConsensbits = new JLabel();
1193     showConsensbits.setFont(LABEL_FONT);
1194     showConsensbits.setHorizontalAlignment(SwingConstants.RIGHT);
1195     showConsensbits.setHorizontalTextPosition(SwingConstants.LEFT);
1196     showConsensbits.setText(MessageManager.getString("label.consensus")
1197             + ":");
1198     showConsensHistogram.setEnabled(false);
1199     showConsensHistogram.setFont(LABEL_FONT);
1200     showConsensHistogram.setHorizontalAlignment(SwingConstants.RIGHT);
1201     showConsensHistogram.setHorizontalTextPosition(SwingConstants.LEFT);
1202     showConsensHistogram.setSelected(true);
1203     showConsensHistogram.setText(MessageManager
1204             .getString("label.histogram"));
1205     showConsensLogo.setEnabled(false);
1206     showConsensLogo.setFont(LABEL_FONT);
1207     showConsensLogo.setHorizontalAlignment(SwingConstants.RIGHT);
1208     showConsensLogo.setHorizontalTextPosition(SwingConstants.LEFT);
1209     showConsensLogo.setSelected(true);
1210     showConsensLogo.setText(MessageManager.getString("label.logo"));
1211     showGroupConsensus.setEnabled(false);
1212     showGroupConsensus.setFont(LABEL_FONT);
1213     showGroupConsensus.setHorizontalAlignment(SwingConstants.RIGHT);
1214     showGroupConsensus.setHorizontalTextPosition(SwingConstants.LEFT);
1215     showGroupConsensus.setSelected(true);
1216     showGroupConsensus.setText(MessageManager.getString("label.consensus"));
1217     showGroupConservation.setEnabled(false);
1218     showGroupConservation.setFont(LABEL_FONT);
1219     showGroupConservation.setHorizontalAlignment(SwingConstants.RIGHT);
1220     showGroupConservation.setHorizontalTextPosition(SwingConstants.LEFT);
1221     showGroupConservation.setSelected(true);
1222     showGroupConservation.setText(MessageManager
1223             .getString("label.conservation"));
1224     showNpTooltip.setEnabled(true);
1225     showNpTooltip.setFont(LABEL_FONT);
1226     showNpTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1227     showNpTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1228     showNpTooltip.setSelected(true);
1229     showNpTooltip.setText(MessageManager
1230             .getString("label.non_positional_features"));
1231     showDbRefTooltip.setEnabled(true);
1232     showDbRefTooltip.setFont(LABEL_FONT);
1233     showDbRefTooltip.setHorizontalAlignment(SwingConstants.RIGHT);
1234     showDbRefTooltip.setHorizontalTextPosition(SwingConstants.LEFT);
1235     showDbRefTooltip.setSelected(true);
1236     showDbRefTooltip.setText(MessageManager
1237             .getString("label.database_references"));
1238     annotations.setFont(LABEL_FONT);
1239     annotations.setHorizontalAlignment(SwingConstants.RIGHT);
1240     annotations.setHorizontalTextPosition(SwingConstants.LEFT);
1241     annotations.setSelected(true);
1242     annotations.setText(MessageManager.getString("label.show_annotations"));
1243     // annotations.setBounds(new Rectangle(169, 12, 200, 23));
1244     annotations.addActionListener(new ActionListener()
1245     {
1246       @Override
1247       public void actionPerformed(ActionEvent e)
1248       {
1249         annotations_actionPerformed(e);
1250       }
1251     });
1252     identity.addActionListener(new ActionListener()
1253     {
1254       @Override
1255       public void actionPerformed(ActionEvent e)
1256       {
1257         annotations_actionPerformed(e);
1258       }
1259     });
1260     showGroupConsensus.addActionListener(new ActionListener()
1261     {
1262       @Override
1263       public void actionPerformed(ActionEvent e)
1264       {
1265         annotations_actionPerformed(e);
1266       }
1267     });
1268     showUnconserved.setFont(LABEL_FONT);
1269     showUnconserved.setHorizontalAlignment(SwingConstants.RIGHT);
1270     showUnconserved.setHorizontalTextPosition(SwingConstants.LEFT);
1271     showUnconserved.setSelected(true);
1272     showUnconserved.setText(MessageManager
1273             .getString("action.show_unconserved"));
1274     showUnconserved.addActionListener(new ActionListener()
1275     {
1276       @Override
1277       public void actionPerformed(ActionEvent e)
1278       {
1279         showunconserved_actionPerformed(e);
1280       }
1281     });
1282
1283     // TODO these are not yet added to / action from Preferences
1284     // JCheckBox shareSelections = new JCheckBox();
1285     // shareSelections.setFont(verdana11);
1286     // shareSelections.setHorizontalAlignment(SwingConstants.RIGHT);
1287     // shareSelections.setHorizontalTextPosition(SwingConstants.LEFT);
1288     // shareSelections.setSelected(true);
1289     // shareSelections.setText(MessageManager
1290     // .getString("label.share_selection_across_views"));
1291     // JCheckBox followHighlight = new JCheckBox();
1292     // followHighlight.setFont(verdana11);
1293     // followHighlight.setHorizontalAlignment(SwingConstants.RIGHT);
1294     // followHighlight.setHorizontalTextPosition(SwingConstants.LEFT);
1295     // // showUnconserved.setBounds(new Rectangle(169, 40, 200, 23));
1296     // followHighlight.setSelected(true);
1297     // followHighlight.setText(MessageManager
1298     // .getString("label.scroll_highlighted_regions"));
1299
1300     seqLimit.setFont(LABEL_FONT);
1301     seqLimit.setHorizontalAlignment(SwingConstants.RIGHT);
1302     seqLimit.setHorizontalTextPosition(SwingConstants.LEFT);
1303     seqLimit.setText(MessageManager.getString("label.full_sequence_id"));
1304     smoothFont.setFont(LABEL_FONT);
1305     smoothFont.setHorizontalAlignment(SwingConstants.RIGHT);
1306     smoothFont.setHorizontalTextPosition(SwingConstants.LEADING);
1307     smoothFont.setText(MessageManager.getString("label.smooth_font"));
1308     scaleProteinToCdna.setFont(LABEL_FONT);
1309     scaleProteinToCdna.setHorizontalAlignment(SwingConstants.RIGHT);
1310     scaleProteinToCdna.setHorizontalTextPosition(SwingConstants.LEADING);
1311     scaleProteinToCdna.setText(MessageManager
1312             .getString("label.scale_protein_to_cdna"));
1313     scaleProteinToCdna.setToolTipText(MessageManager
1314             .getString("label.scale_protein_to_cdna_tip"));
1315     JLabel gapLabel = new JLabel();
1316     gapLabel.setFont(LABEL_FONT);
1317     gapLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1318     gapLabel.setText(MessageManager.getString("label.gap_symbol") + " ");
1319     JLabel fontLabel = new JLabel();
1320     fontLabel.setFont(LABEL_FONT);
1321     fontLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1322     fontLabel.setText(MessageManager.getString("label.font"));
1323     fontSizeCB.setFont(LABEL_FONT);
1324     fontSizeCB.setBounds(new Rectangle(320, 112, 65, 23));
1325     fontStyleCB.setFont(LABEL_FONT);
1326     fontStyleCB.setBounds(new Rectangle(382, 112, 80, 23));
1327     fontNameCB.setFont(LABEL_FONT);
1328     fontNameCB.setBounds(new Rectangle(172, 112, 147, 23));
1329     gapSymbolCB.setFont(LABEL_FONT);
1330     gapSymbolCB.setBounds(new Rectangle(172, 215, 69, 23));
1331     DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
1332     dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
1333     gapSymbolCB.setRenderer(dlcr);
1334
1335     startupCheckbox.setText(MessageManager.getString("action.open_file"));
1336     startupCheckbox.setFont(LABEL_FONT);
1337     startupCheckbox.setHorizontalAlignment(SwingConstants.RIGHT);
1338     startupCheckbox.setHorizontalTextPosition(SwingConstants.LEFT);
1339     startupCheckbox.setSelected(true);
1340     startupFileTextfield.setFont(LABEL_FONT);
1341     startupFileTextfield.setBounds(new Rectangle(172, 310, 330, 20));
1342     startupFileTextfield.addMouseListener(new MouseAdapter()
1343     {
1344       @Override
1345       public void mouseClicked(MouseEvent e)
1346       {
1347         if (e.getClickCount() > 1)
1348         {
1349           startupFileTextfield_mouseClicked();
1350         }
1351       }
1352     });
1353
1354     sortby.setFont(LABEL_FONT);
1355     sortby.setBounds(new Rectangle(172, 260, 155, 21));
1356     JLabel sortLabel = new JLabel();
1357     sortLabel.setFont(LABEL_FONT);
1358     sortLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1359     sortLabel.setText(MessageManager.getString("label.sort_by"));
1360     sortAnnBy.setFont(LABEL_FONT);
1361     sortAnnBy.setBounds(new Rectangle(172, 285, 110, 21));
1362     JLabel sortAnnLabel = new JLabel();
1363     sortAnnLabel.setFont(LABEL_FONT);
1364     sortAnnLabel.setHorizontalAlignment(SwingConstants.RIGHT);
1365     sortAnnLabel.setText(MessageManager.getString("label.sort_ann_by"));
1366     sortAutocalc.setFont(LABEL_FONT);
1367     sortAutocalc.setBounds(new Rectangle(290, 285, 165, 21));
1368
1369     JPanel annsettingsPanel = new JPanel();
1370     annsettingsPanel.setBounds(new Rectangle(173, 13, 320, 96));
1371     annsettingsPanel.setLayout(new FlowLayout(FlowLayout.LEFT, 0, 0));
1372     annsettingsPanel.setBorder(new EtchedBorder());
1373     visualTab.add(annsettingsPanel);
1374     Border jb = new EmptyBorder(1, 1, 4, 5);
1375     annotations.setBorder(jb);
1376     showOccupancy.setBorder(jb);
1377     quality.setBorder(jb);
1378     conservation.setBorder(jb);
1379     identity.setBorder(jb);
1380     showConsensbits.setBorder(jb);
1381     showGroupbits.setBorder(jb);
1382     showGroupConsensus.setBorder(jb);
1383     showGroupConservation.setBorder(jb);
1384     showConsensHistogram.setBorder(jb);
1385     showConsensLogo.setBorder(jb);
1386
1387     JPanel autoAnnotSettings = new JPanel();
1388     annsettingsPanel.add(autoAnnotSettings);
1389     autoAnnotSettings.setLayout(new GridLayout(0, 2));
1390     autoAnnotSettings.add(annotations);
1391     autoAnnotSettings.add(quality);
1392     // second row of autoannotation box
1393     autoAnnotSettings = new JPanel();
1394     annsettingsPanel.add(autoAnnotSettings);
1395
1396     autoAnnotSettings.setLayout(new GridLayout(0, 3));
1397     autoAnnotSettings.add(conservation);
1398     autoAnnotSettings.add(identity);
1399     autoAnnotSettings.add(showOccupancy);
1400     autoAnnotSettings.add(showGroupbits);
1401     autoAnnotSettings.add(showGroupConservation);
1402     autoAnnotSettings.add(showGroupConsensus);
1403     autoAnnotSettings.add(showConsensbits);
1404     autoAnnotSettings.add(showConsensHistogram);
1405     autoAnnotSettings.add(showConsensLogo);
1406
1407
1408
1409     JPanel tooltipSettings = new JPanel();
1410     tooltipSettings.setBorder(new TitledBorder(MessageManager
1411             .getString("label.sequence_id_tooltip")));
1412     tooltipSettings.setBounds(173, 140, 220, 62);
1413     tooltipSettings.setLayout(new GridLayout(2, 1));
1414     tooltipSettings.add(showDbRefTooltip);
1415     tooltipSettings.add(showNpTooltip);
1416     visualTab.add(tooltipSettings);
1417
1418     wrap.setFont(LABEL_FONT);
1419     wrap.setHorizontalAlignment(SwingConstants.TRAILING);
1420     wrap.setHorizontalTextPosition(SwingConstants.LEADING);
1421     wrap.setText(MessageManager.getString("label.wrap_alignment"));
1422     rightAlign.setFont(LABEL_FONT);
1423     rightAlign.setForeground(Color.black);
1424     rightAlign.setHorizontalAlignment(SwingConstants.RIGHT);
1425     rightAlign.setHorizontalTextPosition(SwingConstants.LEFT);
1426     rightAlign.setText(MessageManager.getString("label.right_align_ids"));
1427     idItalics.setFont(LABEL_FONT_ITALIC);
1428     idItalics.setHorizontalAlignment(SwingConstants.RIGHT);
1429     idItalics.setHorizontalTextPosition(SwingConstants.LEADING);
1430     idItalics.setText(MessageManager
1431             .getString("label.sequence_name_italics"));
1432     openoverv.setFont(LABEL_FONT);
1433     openoverv.setActionCommand(MessageManager
1434             .getString("label.open_overview"));
1435     openoverv.setHorizontalAlignment(SwingConstants.RIGHT);
1436     openoverv.setHorizontalTextPosition(SwingConstants.LEFT);
1437     openoverv.setText(MessageManager.getString("label.open_overview"));
1438     JPanel jPanel2 = new JPanel();
1439     jPanel2.setBounds(new Rectangle(7, 17, 158, 310));
1440     jPanel2.setLayout(new GridLayout(14, 1));
1441     jPanel2.add(fullScreen);
1442     jPanel2.add(openoverv);
1443     jPanel2.add(seqLimit);
1444     jPanel2.add(rightAlign);
1445     jPanel2.add(fontLabel);
1446     jPanel2.add(showUnconserved);
1447     jPanel2.add(idItalics);
1448     jPanel2.add(smoothFont);
1449     jPanel2.add(scaleProteinToCdna);
1450     jPanel2.add(gapLabel);
1451     jPanel2.add(wrap);
1452     jPanel2.add(sortLabel);
1453     jPanel2.add(sortAnnLabel);
1454     jPanel2.add(startupCheckbox);
1455     visualTab.add(jPanel2);
1456     visualTab.add(startupFileTextfield);
1457     visualTab.add(sortby);
1458     visualTab.add(sortAnnBy);
1459     visualTab.add(sortAutocalc);
1460     visualTab.add(gapSymbolCB);
1461     visualTab.add(fontNameCB);
1462     visualTab.add(fontSizeCB);
1463     visualTab.add(fontStyleCB);
1464     return visualTab;
1465   }
1466
1467   protected void autoIdWidth_actionPerformed()
1468   {
1469     // TODO Auto-generated method stub
1470
1471   }
1472
1473   protected void userIdWidth_actionPerformed()
1474   {
1475     // TODO Auto-generated method stub
1476
1477   }
1478
1479   protected void maxColour_actionPerformed(JPanel panel)
1480   {
1481   }
1482
1483   protected void minColour_actionPerformed(JPanel panel)
1484   {
1485   }
1486
1487   protected void showunconserved_actionPerformed(ActionEvent e)
1488   {
1489     // TODO Auto-generated method stub
1490
1491   }
1492
1493   /**
1494    * DOCUMENT ME!
1495    *
1496    * @param e
1497    *          DOCUMENT ME!
1498    */
1499   public void ok_actionPerformed(ActionEvent e)
1500   {
1501   }
1502
1503   /**
1504    * DOCUMENT ME!
1505    *
1506    * @param e
1507    *          DOCUMENT ME!
1508    */
1509   public void cancel_actionPerformed(ActionEvent e)
1510   {
1511   }
1512
1513   /**
1514    * DOCUMENT ME!
1515    *
1516    * @param e
1517    *          DOCUMENT ME!
1518    */
1519   public void annotations_actionPerformed(ActionEvent e)
1520   {
1521   }
1522
1523   /**
1524    * DOCUMENT ME!
1525    */
1526   public void startupFileTextfield_mouseClicked()
1527   {
1528   }
1529
1530   public void newLink_actionPerformed(ActionEvent e)
1531   {
1532
1533   }
1534
1535   public void editLink_actionPerformed(ActionEvent e)
1536   {
1537
1538   }
1539
1540   public void deleteLink_actionPerformed(ActionEvent e)
1541   {
1542
1543   }
1544
1545   public void defaultBrowser_mouseClicked(MouseEvent e)
1546   {
1547
1548   }
1549
1550   public void linkURLList_keyTyped(KeyEvent e)
1551   {
1552
1553   }
1554
1555   public void useProxy_actionPerformed()
1556   {
1557     boolean enabled = useProxy.isSelected();
1558     portLabel.setEnabled(enabled);
1559     serverLabel.setEnabled(enabled);
1560     proxyServerTB.setEnabled(enabled);
1561     proxyPortTB.setEnabled(enabled);
1562   }
1563
1564   /**
1565    * Customer renderer for JTable: supports column of radio buttons
1566    */
1567   public class RadioButtonRenderer extends JRadioButton implements
1568           TableCellRenderer
1569   {
1570     public RadioButtonRenderer()
1571     {
1572       setHorizontalAlignment(CENTER);
1573       setToolTipText(MessageManager.getString("label.urltooltip"));
1574     }
1575
1576     @Override
1577     public Component getTableCellRendererComponent(JTable table,
1578             Object value, boolean isSelected, boolean hasFocus, int row,
1579             int column)
1580     {
1581       setSelected((boolean) value);
1582
1583       // set colours to match rest of table
1584       if (isSelected)
1585        {
1586          setBackground(table.getSelectionBackground());
1587          setForeground(table.getSelectionForeground());
1588        }
1589        else
1590        {
1591          setBackground(table.getBackground());
1592          setForeground(table.getForeground());
1593       }
1594       return this;
1595     }
1596   }
1597
1598   /**
1599    * Customer cell editor for JTable: supports column of radio buttons in
1600    * conjunction with renderer
1601    */
1602   public class RadioButtonEditor extends AbstractCellEditor implements
1603             TableCellEditor
1604     {
1605       private JRadioButton button = new JRadioButton();
1606
1607       public RadioButtonEditor()
1608       {
1609       button.setHorizontalAlignment(SwingConstants.CENTER);
1610       this.button.addActionListener(new ActionListener()
1611         {
1612           @Override
1613           public void actionPerformed(ActionEvent e)
1614           {
1615             fireEditingStopped();
1616           }
1617         });
1618       }
1619
1620       @Override
1621       public Component getTableCellEditorComponent(JTable table,
1622               Object value, boolean isSelected, int row, int column)
1623       {
1624       button.setSelected((boolean) value);
1625         return button;
1626       }
1627
1628       @Override
1629       public Object getCellEditorValue()
1630       {
1631       return button.isSelected();
1632       }
1633
1634   }
1635 }